Magnesium in PDB 7xmb: Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113

Enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113

All present enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113:
7.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113, PDB code: 7xmb was solved by Y.Nishida, K.Shinzawa-Itoh, N.Mizuno, T.Kumasaka, S.Yoshikawa, T.Tsukihara, Y.Shintani, S.Takashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.097, 204.337, 177.933, 90, 90, 90
R / Rfree (%) 17.8 / 20.4

Other elements in 7xmb:

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 (pdb code 7xmb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113, PDB code: 7xmb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7xmb

Go back to Magnesium Binding Sites List in 7xmb
Magnesium binding site 1 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:14.5
occ:1.00
 O B:HOH770 2.1 20.2 1.0
OE1 B:GLU198 2.1 27.2 1.0
OD2 A:ASP369 2.1 22.2 1.0
O B:HOH763 2.1 20.8 1.0
O B:HOH826 2.1 19.9 1.0
NE2 A:HIS368 2.2 24.4 1.0
CD2 A:HIS368 3.1 19.7 1.0
CE1 A:HIS368 3.1 27.4 1.0
CD B:GLU198 3.3 35.2 1.0
CG A:ASP369 3.3 30.9 1.0
OE2 B:GLU198 3.9 35.7 1.0
O B:SER197 3.9 25.8 1.0
O A:HOH903 4.0 24.2 1.0
O B:HOH831 4.0 46.3 0.5
CB A:ASP369 4.1 24.7 1.0
ND1 A:HIS368 4.2 18.0 1.0
CG A:HIS368 4.2 24.6 1.0
OD1 A:ASP369 4.2 27.1 1.0
O A:HOH806 4.3 21.0 1.0
OD2 B:ASP173 4.4 29.2 1.0
O A:HOH764 4.4 23.5 1.0
CG B:GLU198 4.4 19.7 1.0
O A:HOH799 4.4 25.4 1.0
OD1 B:ASP173 4.5 25.9 1.0
OG1 A:THR294 4.5 29.8 1.0
O A:HOH734 4.6 26.1 1.0
CB B:GLU198 4.6 29.3 1.0
O B:HOH829 4.6 37.0 0.5
CG B:ASP173 4.8 35.7 1.0
O A:HOH779 4.8 20.4 0.7
CA B:GLU198 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in 7xmb

Go back to Magnesium Binding Sites List in 7xmb
Magnesium binding site 2 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, the Structure Complexed with An Allosteric Inhibitor T113 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:16.1
occ:1.00
 OD2 N:ASP369 2.1 21.8 1.0
OE1 O:GLU198 2.1 30.4 1.0
O O:HOH743 2.1 22.7 1.0
O O:HOH788 2.1 23.3 1.0
O O:HOH740 2.1 26.0 1.0
NE2 N:HIS368 2.2 27.8 1.0
CD2 N:HIS368 3.1 22.9 1.0
CE1 N:HIS368 3.1 30.5 1.0
CD O:GLU198 3.3 44.3 1.0
CG N:ASP369 3.3 50.7 1.0
O O:SER197 3.8 27.8 1.0
OE2 O:GLU198 3.9 35.5 1.0
O N:HOH908 3.9 28.4 1.0
CB N:ASP369 4.0 19.6 1.0
ND1 N:HIS368 4.2 18.9 1.0
CG N:HIS368 4.2 26.2 1.0
O N:HOH860 4.2 28.5 1.0
OD1 N:ASP369 4.3 25.2 1.0
O N:HOH732 4.3 24.4 1.0
OD2 O:ASP173 4.3 31.0 1.0
CG O:GLU198 4.4 23.9 1.0
OD1 O:ASP173 4.5 24.6 1.0
O N:HOH786 4.5 30.2 1.0
OG1 N:THR294 4.5 32.8 1.0
CB O:GLU198 4.5 26.4 1.0
O N:HOH779 4.6 23.8 1.0
O N:HOH803 4.8 18.9 0.7
CG O:ASP173 4.8 31.7 1.0
CA O:GLU198 4.8 28.0 1.0
C O:SER197 4.9 41.8 1.0

Reference:

Y.Nishida, S.Yanagisawa, R.Morita, H.Shigematsu, K.Shinzawa-Itoh, H.Yuki, S.Ogasawara, K.Shimuta, T.Iwamoto, C.Nakabayashi, W.Matsumura, H.Kato, C.Gopalasingam, T.Nagao, T.Qaqorh, Y.Takahashi, S.Yamazaki, K.Kamiya, R.Harada, N.Mizuno, H.Takahashi, Y.Akeda, M.Ohnishi, Y.Ishii, T.Kumasaka, T.Murata, K.Muramoto, T.Tosha, Y.Shiro, T.Honma, Y.Shigeta, M.Kubo, S.Takashima, Y.Shintani. Identifying Antibiotics Based on Structural Differences in the Conserved Allostery From Mitochondrial Heme-Copper Oxidases. Nat Commun V. 13 7591 2022.
ISSN: ESSN 2041-1723
PubMed: 36481732
DOI: 10.1038/S41467-022-34771-Y
Page generated: Thu Oct 3 12:30:41 2024

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